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Expanding OBIS beyond
species occurrence data, with
an extension for
environmental data
Photo credits Molly Timmers - NOAA...
46,000,000species observations
4,600,000 sampling events
3,200,000 sampling stations
117,000marine species
1,900databases ...
Census of Marine Life
2000 - 2010
OBIS was established as the data repository
and information dissemination system for
CoML
OBIS @ UNESCO-IOC
In June 2009, the 25th Session of the IOC Assembly
decided through Resolution XXV-4 to adopt OBIS as
par...
Darwin Core Archive
Occurrence core EML Meta.xml
DwC terms managed by TDWG
1. eventDate
2. decimalLongitude
3. decimalLati...
Sampling more data than
just species occurrence
Core sample from a Van
Veen grab
Water sample from
a Niskin bottle plankto...
XXIII session of the IOC Committee for
IODE, March 2015
Recommendation IODE-XXIII.4
ESTABLISHMENT OF THE IODE PILOT PROJEC...
OBIS-ENV-DATA
1st workshop October 2015
OBIS-ENV-DATA involves 11 institutions from
10 countries in North-America, South-A...
ABIOTIC READINGS
Environmental:
Light Conditions, Ice Coverage, Secchi Disc Depth, Turbidity, Light Transmission,
Wind Dir...
Integrated Publishing Toolkit
Star Schema
Occurrence core
MoF Extension
1
Event core
Occurrence
Extension
MoF Extension
1 ...
What we needed
OBIS-ENV-DATA
event 1
occurrence 1
occurrence 2
measurement 1
measurement 2
Not compatible
with star schema...
Option 1
event 1 occurrence 1
event 1 occurrence 2
measurement 1
measurement 2
measurement 1
Occurrence Core MeasurementOr...
Option 2
event 1
measurement 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence ...
Option 3
event 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence Core
measureme...
event 1
occurrence 1
occurrence 2
measurement 1
measurement 2
Occurrence Core MeasurementOrFacts Extension
Option 4
OBIS-E...
Option 5
event 1
measurement 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence ...
event 1
measurement 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence Extension...
Event Core
Occurrence Extension
Extended
MeasurementOrFact Extension
eventID
eventID
eventID
occurrenceID
occurrenceIDOBIS...
Extended MeasurementOrFact(s) Extension allows for
parameter standardization (linking to external URI of a
controlled voca...
Event-ID Occurrence-ID MoF-Type MoF-Value MoF-Unit
1 Sampling device name Van-Veen grab
1 Area sampled 0.112 m2
1 Sample v...
ID
Occurre
nce-ID
MoF-Type MoF-TypeID MoF-Value MoF-ValueID MoF-Unit MoF-UnitID
1 Sampling device name L19/current/
SDNKG0...
Event
1
Event
1.1
Event
1.1.1
MoF
A1
MoF
B1
Occ
1
Occ
2
Occ
3
MoF
B2
MoF
B3
OBIS-ENV-DATA
EVENT HIERARCHY makes it possibl...
CTD and Niskin bottles
Each separate sensor reading can be considered
a sub-event of the CTD cast. The Niskin bottle
with ...
CTD and plankton net
If a CTD sensor was placed on a sampling net,
the parentEventID to which the sensor
readings are link...
Animal telemetry
Event1
(entire track)
Event1.1
(position1)
Event1.2
(position2)
Event1.3
(position3)
OTN tags
Each separa...
Video Plankton Recorder
Event1
(tow)
Event1.1
(4 seconds)
Event1.1.1
(image1)
MoF1.1
MoF1.1.1
Occ 1.1.1 DwC:AssociatedMedi...
Pilot datasets on ipt.iobis.org/obis-env
download
versioning
upload
PUBLISH
OBIS 2.0 developments
github.com/iobis/api-docs
github.com/iobis/robis
github.com/iobis/pyobis
github.com/iobis/training
@WrdAppltns
THANK YOU
info@iobis.org
WWW www.iobis.org
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Expanding OBIS beyond species occurrence data, including sampling event facts and measurements related to the environment

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Developments of a new OBIS data standard, IODE pilot project OBIS-ENV-DATA

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Expanding OBIS beyond species occurrence data, including sampling event facts and measurements related to the environment

  1. 1. Expanding OBIS beyond species occurrence data, with an extension for environmental data Photo credits Molly Timmers - NOAA w.appeltans@unesco.org International Oceanographic Data and Information Exchange Co-authors: OBIS-ENV-DATA project consortium
  2. 2. 46,000,000species observations 4,600,000 sampling events 3,200,000 sampling stations 117,000marine species 1,900databases in 1central global database 500data providers, 56countries 1,000papers have cited OBIS (9) (4) UNGA resolution (A/RES/70) notes with appreciation the contribution of OBIS to marine scientific research. Some Statistics
  3. 3. Census of Marine Life 2000 - 2010 OBIS was established as the data repository and information dissemination system for CoML
  4. 4. OBIS @ UNESCO-IOC In June 2009, the 25th Session of the IOC Assembly decided through Resolution XXV-4 to adopt OBIS as part of IODE, because: Knowledge of the ocean's biodiversity is of such importance to national and global environmental issues that the responsibility for its continuing success should be assumed by governments. Intergovernmental Oceanographic Commission Established in 1960 148 Member States UNCLOS: IOC = competent international organization for Marine Scientific Research and Transfer of Marine Technology UN focal point for ocean science, ocean observations and services, data and information exchange and capacity building
  5. 5. Darwin Core Archive Occurrence core EML Meta.xml DwC terms managed by TDWG 1. eventDate 2. decimalLongitude 3. decimalLatitude 4. scientificName 5. scientificNameID 6. occurrenceStatus 7. basisOfRecord WHEN WHERE WHAT BY WHO HOW MANY POINTS, LINES, POLYGONS DEPTH SAMPLINGPROTOCOL OBIS DATA STANDARD
  6. 6. Sampling more data than just species occurrence Core sample from a Van Veen grab Water sample from a Niskin bottle plankton net with CTD Video plankton recorder OTN tags
  7. 7. XXIII session of the IOC Committee for IODE, March 2015 Recommendation IODE-XXIII.4 ESTABLISHMENT OF THE IODE PILOT PROJECT EXPANDING OBIS WITH ENVIRONMENTAL DATA (OBIS-ENV-DATA)
  8. 8. OBIS-ENV-DATA 1st workshop October 2015 OBIS-ENV-DATA involves 11 institutions from 10 countries in North-America, South-America, Europe, Africa and Oceania. In collaboration with 14 pilot datasets
  9. 9. ABIOTIC READINGS Environmental: Light Conditions, Ice Coverage, Secchi Disc Depth, Turbidity, Light Transmission, Wind Direction, Bottom Temperature, Surface Salinity Sediment Sample: Metal Concentrations, Sediment Grain Sizes Water Sample: Nutrient (NO3) and Chlorophyll a Concentration, Temperature, Salinity Sensor based: CTD profiles, tracking data, data derived from sensors attached to the sampling device SAMPLING GEAR RMT-1 net: zooplankton, fish CTD-Tracker: marine mammals Van Veen Grab: macrobenthos Sorbe sledge: hyperbenthos VPR: plankton MOCNESS net: zooplankton Throw-trap: zooplankton Niskin bottle: phytoplankton 14 pilot datasets
  10. 10. Integrated Publishing Toolkit Star Schema Occurrence core MoF Extension 1 Event core Occurrence Extension MoF Extension 1 1 MoF = Measurement or Fact ∞ ∞ ∞ MoF addresses methods, abiotic and biological measurements Sample event is the DwC core
  11. 11. What we needed OBIS-ENV-DATA event 1 occurrence 1 occurrence 2 measurement 1 measurement 2 Not compatible with star schema Event Core MeasurementOrFacts ExtensionOccurrence Extension
  12. 12. Option 1 event 1 occurrence 1 event 1 occurrence 2 measurement 1 measurement 2 measurement 1 Occurrence Core MeasurementOrFacts Extension event 1 occurrence 1 occurrence 2 measurement 1 measurement 2 OBIS-ENV-DATA Event MoF needs to be repeated for each occurrence record
  13. 13. Option 2 event 1 measurement 1 measurement 2 Event Core MeasurementOrFacts Extension occurrence 1 occurrence 2 Occurrence Extension Not possible when both abundance and biomass measurements are made and can’t record measurements or facts related to the occurrence OBIS-ENV-DATA
  14. 14. Option 3 event 1 measurement 2 Event Core MeasurementOrFacts Extension occurrence 1 occurrence 2 Occurrence Core measurement 1 MeasurementOrFacts Extension Archive 1 Archive 2 Not possible because Event Core requires an occurrence extension file, and 2 archives for one dataset is confusing, need links between archives OBIS-ENV-DATA Creating 2 Archives one for Events and abiotic and one for Occurrences and biological measurements
  15. 15. event 1 occurrence 1 occurrence 2 measurement 1 measurement 2 Occurrence Core MeasurementOrFacts Extension Option 4 OBIS-ENV-DATA Is abusing the Occurrence Core Creating dummy occurrence records, treat as an event record
  16. 16. Option 5 event 1 measurement 1 measurement 2 Event Core MeasurementOrFacts Extension occurrence 1 occurrence 2 Occurrence Extension event 1_1 event 1_2 OBIS-ENV-DATA Complex and not intuitive. Creating a dummy event for each occurrence extension record
  17. 17. event 1 measurement 1 measurement 2 Event Core MeasurementOrFacts Extension occurrence 1 occurrence 2 Occurrence Extension OBIS-ENV-DATA We need to customize the MoF Extension
  18. 18. Event Core Occurrence Extension Extended MeasurementOrFact Extension eventID eventID eventID occurrenceID occurrenceIDOBIS-ENV-DATA Option 6
  19. 19. Extended MeasurementOrFact(s) Extension allows for parameter standardization (linking to external URI of a controlled vocabulary) ID: the identifier used by DwC-A standard to link the eMoF to the Core file. occurrenceID (new): identifier to link the eMoF with the occurrence extension. measurementType: The nature of the measurement, fact, characteristic, or assertion. measurementTypeID (new): An identifier for the measurementType (global unique identifier, URI) measurementValue: The value of the measurement, fact, characteristic, or assertion. measurementValueID (new): An identifier for facts stored in the column measurementValue (global unique identifier, URI) measurementAccuracy: The description of the potential error associated with the measurementValue. measurementUnit: The value of the measurement, fact, characteristic, or assertion. measurementUnitID (new): An identifier for the measurementUnit (global unique identifier, URI) measurementDeterminedDate: The date on which the MeasurementOrFact was made. measurementDeterminedBy: A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact. measurementMethod: A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. measurementRemarks: Comments or notes accompanying the MeasurementOrFact.
  20. 20. Event-ID Occurrence-ID MoF-Type MoF-Value MoF-Unit 1 Sampling device name Van-Veen grab 1 Area sampled 0.112 m2 1 Sample volume 20 L 1 Sieze mesh size 250 µm 1 Biological entity size sampled 250-1000 µm 1 1 Ash-free dry weight biomass 0.2 Kg/m2 1 1 ObservedindividualCount 112 individuals 1 1 Abundance 1000 individuals/m2 1 1 lifeStage juvenile EXAMPLE benthic sample Van Veen grab Extended MeasurementOrFact(s) Extension
  21. 21. ID Occurre nce-ID MoF-Type MoF-TypeID MoF-Value MoF-ValueID MoF-Unit MoF-UnitID 1 Sampling device name L19/current/ SDNKG01/ Van-Veen grab L22/current/ TOOL0653/ 1 Area sampled P01/current/ AREABEDS/ 0.112 m2 P06/current/U MSQ/ 1 Sample volume P01/current/ VOLXXXXX/ 20 L P06/current/U LIT/ 1 Sieze mesh size 250 µm P06/current/U MIC/ 1 Biological entity size sampled 250-1000 µm P06/current/U MIC/ 1 1 Ash-free dry weight biomass P01/current/ SDBIOL03/ 0.2 Kg/m2 P06/current/K MP2/ 1 1 ObservedindividualCou nt P01/current/ OCOUNT01/ 112 individuals 1 1 Abundance P01/current/ SDBIOL02/ 1000 individuals/ m2 P06/current/U PMS/ 1 1 lifeStage S11/ juvenile S11/current/ S1127/ Linking to external URI of a controlled vocabulary for parameter standardization
  22. 22. Event 1 Event 1.1 Event 1.1.1 MoF A1 MoF B1 Occ 1 Occ 2 Occ 3 MoF B2 MoF B3 OBIS-ENV-DATA EVENT HIERARCHY makes it possible to record differences in sampling time, location, and depth while still grouping these samples together to the same station visit MoF A2
  23. 23. CTD and Niskin bottles Each separate sensor reading can be considered a sub-event of the CTD cast. The Niskin bottle with the biological sample can be linked to the subevent of the CTD cast. Event1 (station) Event1.1 (depth1) Event1.2 (depth2) Event1.3 (depth3) MoF1 MoF1.1 MoF1.2 MoF1.3 Occ 1.3 thermocline
  24. 24. CTD and plankton net If a CTD sensor was placed on a sampling net, the parentEventID to which the sensor readings are linked may represent the deployment of this net, so biological data can be linked directly to this parentEventID. Event1 (tow) Event1.1 (position1) Event1.2 (position2) Event1.3 (position3) MoF1.1 MoF1.2 MoF1.3 Bongo nets and CTD unit being deployed from theHenry Bigelow. (Photo by Sammi Ocher, Northeastern University) Occ 1 MoF1
  25. 25. Animal telemetry Event1 (entire track) Event1.1 (position1) Event1.2 (position2) Event1.3 (position3) OTN tags Each separate sensor reading can be considered a sub-event of a parent event which can be linked to an occurrence record for the animal. The parent event may represent the entire tagging sequence of the animal, or a grouping of sorts for readings recorded at the same period and area, which are then grouped to make up the entire sequence. MoF1 Occ 1 MoF1.1 MoF1.2 MoF1.3
  26. 26. Video Plankton Recorder Event1 (tow) Event1.1 (4 seconds) Event1.1.1 (image1) MoF1.1 MoF1.1.1 Occ 1.1.1 DwC:AssociatedMedia VPR takes 30 images/sec, software groups by 4 seconds
  27. 27. Pilot datasets on ipt.iobis.org/obis-env download versioning upload PUBLISH
  28. 28. OBIS 2.0 developments github.com/iobis/api-docs github.com/iobis/robis github.com/iobis/pyobis github.com/iobis/training
  29. 29. @WrdAppltns THANK YOU info@iobis.org WWW www.iobis.org

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